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- PDB-2yt5: Solution structure of the PHD domain of Metal-response element-bi... -

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Basic information

Entry
Database: PDB / ID: 2yt5
TitleSolution structure of the PHD domain of Metal-response element-binding transcription factor 2
ComponentsMetal-response element-binding transcription factor 2
KeywordsTRANSCRIPTION / PHD domain / Metal-response element-binding transcription factor 2 / Zinc-regulated factor 1 / ZiRF1 / Metal-response element DNA-binding protein M96 / Metal-regulatory transcription factor 2 / PCL2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


PRC2 methylates histones and DNA / segment specification / stem cell population maintenance / epigenetic regulation of gene expression / methylated histone binding / cellular response to leukemia inhibitory factor / transcription corepressor binding / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific ...PRC2 methylates histones and DNA / segment specification / stem cell population maintenance / epigenetic regulation of gene expression / methylated histone binding / cellular response to leukemia inhibitory factor / transcription corepressor binding / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromatin organization / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
MTF2, PHD domain 1 / MTF2, PHD domain 2 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...MTF2, PHD domain 1 / MTF2, PHD domain 2 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metal-response element-binding transcription factor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMasuda, K. / Muto, Y. / Isono, K. / Watanabe, S. / Harada, T. / Kigawa, T. / Koseki, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PHD domain of Metal-response element-binding transcription factor 2
Authors: Masuda, K. / Muto, Y. / Isono, K. / Watanabe, S. / Harada, T. / Kigawa, T. / Koseki, H. / Yokoyama, S.
History
DepositionApr 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-response element-binding transcription factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4103
Polymers7,2791
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Metal-response element-binding transcription factor 2 / Zinc-regulated factor 1 / ZiRF1 / Metal-response element DNA-binding protein M96 / Metal-regulatory ...Zinc-regulated factor 1 / ZiRF1 / Metal-response element DNA-binding protein M96 / Metal-regulatory transcription factor 2 / PCL2


Mass: 7279.103 Da / Num. of mol.: 1 / Fragment: PHD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Mtf2 / Plasmid: P061010-06 / References: UniProt: Q02395
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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